EXPR_COUNT_VALUES
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010001924 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 2 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1). Genes that have values greater than or equal to lower cut-off: 100.0 in that at least 1 out of 2 samples (“All Targets Value”) were chosen for data analysis.
2022-07-20 | GSE208583 | GEO
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains CITE-seq data (surface protein and cytosolic RNA content) data from two biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11549 | biostudies-arrayexpress
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains fetal liver CITE-seq (surface protein and cytosolic RNA content) data from six biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11613 | biostudies-arrayexpress
Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains embryonic liver CITE-seq (surface protein and cytosolic RNA content) data from three biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.
2022-12-08 | E-MTAB-11618 | biostudies-arrayexpress
Project description:Evaluation of modulation of the innate immune response during H1N1 infection. The modulatory effect of Single-stranded oligonucleotides (ssON) on monocyte-derived dendritic cells (MoDCs) are evaluated. RNAseq data are used to study the effect on the transcriptome of MoDCs, during infection with simultaneous addition of ssON. Further mechanistic information are added via RNAseq data on poly I:C stimulated MoDCs (Toll-Like Receptor 3 agonist). Control samples are included to perform differential expression analysis. Provided are the fastq files, obtained in the following manner: The RNA sequencing was performed with the TruSeq RiboZero kit from Illumina, 25 M reads per sample and 2x125bp. Read quality were assessed using FastQC (Version 0.11.5) Trim Galore (Version 0.3.6) was used for adapter removal and quality trimming with a quality threshold of 20 on the Phred scale. Count files was created out of the trimmed fastq by mapping high-quality reads to Homo sapiens UCSC hg38 (GRCh38.77) reference genome using STAR aligner (version 2.5) with default values and the parameter out Reads Unmapped set to Fastx in order to extract the unmapped reads. After STAR alignment, the count data for the aligned reads were generated with HTSeq-count (version 0.6.1). The-m parameter was set to union.
2019-05-03 | E-MTAB-7803 | biostudies-arrayexpress
Project description:For single cell RNA sequencing analysis, whole cell population isolated from two breast cancer bone metastases and associated organoid models were analyzed by 10X genomic single cell RNA platform. Raw BCL files from Novaseq6000 was converted to FASTQ files with cellranger (Version: 3.1.0) mkfastq function. Cellranger count function was then applied for read alignment, barcode and UMI counting using GRCh38 as reference. scCB2 and DoubletFinder were used to predict and remove empty droplets and doublets of single cell data. Cells with number of features less 300 and more than 9000 were further filtered out based on the distribution of number of features. For bulk RNA sequencing, RNA were extracted from FFPE preserved primary tumor and bone metastasis. Library was prepared with TruSeq Stranded mRNA for FFPE kit, and sequenced by NextSeq 500 with high output 150 cycle kit.
2022-02-08 | GSE190772 | GEO
Project description:10 adult participants of dose group 3x10^6 pfu, and 10 participants of dose group 20x10^6 pfu. Reads were aligned to the human reference assembly (GRCh38.p7) using STAR software (v2.4.2a; option '--quantMode GeneCounts'). Gene annotation was obtained from Ensembl (release 79, ensemble.org). VOOM+Limma analysis (R software, version 3.2.2) was used to assess differential gene expression at each post-vaccination day (d1, d3 and d7) against baseline (d0). Next, we intergreted gene expression data and antibody response using an sPLS algorithm, in order to down-select genes correlating with multivariate antibody responses at days 28, 54, 84,180.
2017-08-29 | GSE97590 | GEO
Project description:Small RNAs (<100 bases in length) were purified from total RNA samples using the miRNeasy kit (Qiagen), and multiplexed miRNA libraries were prepared using a previously described protocol and sequenced on a HiSeq 2000 (Illumina). Image analysis, base calling, demultiplexing and conversion of BCL to FASTQ format were carried out using CASAVA 1.8.2 software (Illumina). Adaptor sequences were removed using mirExpress software. Fastq were 3p-adaptor trimmed. The sequences were then aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a), allowing no mismatch with reference. Reads were counted using HTSeq-count (HTSeq v 0.6.1p1 Python package) using “intersection-strict” mode, to count mature miRNA abundance according to miRbase v.20.
2020-08-12 | E-MTAB-6553 | biostudies-arrayexpress
Project description:Purpose: The aim of this study was to compare the differentially expressed genes under thalidomide treatment in limb buds. Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 81 database. Alignment was performed using STAR (version 2.4.2a ). Expression estimation carried out using cufflinks program (version 2.2.1).Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1). Heat maps were generated for gene expression analysis using R statistical software.
2021-12-01 | GSE80309 | GEO
Project description:Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.
2022-12-07 | E-MTAB-11673 | biostudies-arrayexpress